|
| Status |
Public on Jul 16, 2013 |
| Title |
L1 |
| Sample type |
RNA |
| |
|
| Source name |
low intramuscular fatty acid composition
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Liver
gender: Female
intramuscular fatty acid composition: low (L)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From the 10 selected animals, total RNA was isolated from liver using the RiboPureTM Isolation of High Quality Total RNA (Ambion®, Austin, TX) following the manufacturer’s recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, USA) and checked for purity and integrity in a Bioanalyzer-2100 (Agilent Technologies, Inc., Santa Clara CA, USA).
|
| Label |
biotin
|
| Label protocol |
Samples (12μg of cRNA with biotin-conjugated nucleotide) were chemically fragmented and labeled using the Fragmentation Buffer included in the IVT Express kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Microrarrays were hybridized and scanned at the Institut de Recerca Hospital Universitari Vall d'Hebron (Barcelona, Spain). Approximately 10μg of fragmented cRNA was hybridzed per array using the Affymetrix hybridization kit.Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
LI074.CEL
|
| Data processing |
Expression data were generated with Gene-Chip Operating Software (GCOS). Probes were adjusted for background noises and normalized using the GCRMA R package RMA algorithm was used to normalize the arrays and summarized the probes.
|
| |
|
| Submission date |
Jun 08, 2012 |
| Last update date |
Jul 16, 2013 |
| Contact name |
Yuliaxis Ramayo-Caldas |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre for Research in Agricultural Genomics
|
| Department |
Animal Genetics
|
| Street address |
Centre for Research in Agricultural Genomics
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE38588 |
Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition |
|
